I performed taxonomic analysis on the single end reads which is for the V4 region. Earlier when I did the taxonomic analysis (here) using paired end reads for the same samples, I found almost all of the features had corresponded to either d_0_bacteria or unassigned. I assumed it might be because I did not successfully merge them.
Hence on repeating the same steps with the single end reads, for few features I did get family and genus level classification (but still very low). The remaining are still unassigned (which is from the host) while for several features I still see d_0_bacteria: what does this mean? Can anything be done to improve this classification? The now improved taxonomy file for single end reads is below.
taxonomySE.qzv (1.3 MB)